Abstract P5-11-05: Pregnancy-induced epigenetic changes in the insulin-like growth factor signaling pathway

Prevention will prove to be the single most effective way of eradicating breast cancer. Currently, the most effective natural breast cancer prevention is an early first full term pregnancy. While it is not feasible to use pregnancy to protect women from breast cancer, understanding how the protective effect is elicited will inform the development of new prevention strategies. Women who were pregnant in their twenties are protected thirty to forty years later creating a complicated mechanism to tease out experimentally. In order to understand the long-term protection we have investigated epigenetics, specifically DNA methylation, which is known to be stable over long periods of time. A cohort (Parous) of female FVB mice were bred, gave birth, and pups were weaned. A control group (Nulliparpous) never saw male mice. Mammary glands were harvested immediately or 6 months after involution. These two time points allowed us to identify changes in DNA methylation that occurred in response to pregnancy, and additionally, changes that lasted long after parturition. DNA was isolated, and genome-wide DNA methylation was assessed using bisulfite-conversion and SureSelect Methyl-Seq. Bismark v0.7.12 was used for alignment of pair-end reads, followed by the R package "methylKit" for quality control and data analysis. A mapping efficiency of 50%∼68.1% was achieved with 89,512,619 base pairs covered. CpG Pearson correlation plots and PCA analysis showed global similarity between samples. We then conducted a logistic regression to ascertain parity-induced differentially methylated regions and identified 153 and 236 persistently hypomethylated and hypermethylated genes, respectively. Among the differentially methylated genes were many signaling molecules involved in growth factor signal transduction, including insulin-like growth factor 1 and 2 receptors (IGF1R and IGF2R). It has previously been shown that circulating IGF1 levels are reduced in parous women, and similarly the growth hormone/IGF axis is altered in rodent models. Collectively, these findings suggest that the IGF pathway is regulated at multiple levels during pregnancy, and that its modification might be critical in the protective role of pregnancy. We are currently following up on these data, including protein analysis of the IGF pathway members and downstream signaling molecules in human specimens. Finally, we are expanding our analysis to additional genes and pathways epigenetically altered by pregnancy, with the ultimate goal to develop new prevention strategies.

Citation Format: Tiffany A Katz, Serena G Liao, Thushangi Pathiraja, Robert K Dearth, George C Tseng, Steffi Oesterreich, Adrian V Lee. Pregnancy-induced epigenetic changes in the insulin-like growth factor signaling pathway [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P5-11-05.

Abstract P2-09-02: Epigenetic Regulation of histone variants - a role in hormone therapy resistant breast cancer?

OBJECTIVE To utilize a genome wide approach to characterize epigenetic changes associated with resistance to estrogen deprivation, thus mimicking resistant to AIs.

BACKGROUND Mechanisms of endocrine resistance include the activation of growth factor receptor pathways, overexpression of ER co-activators, and metabolic resistance due to polymorphisms in metabolizing enzymes. Recently, epigenetic mechanisms have been investigated to explain endocrine resistance. The majority of mechanisms for acquired resistance have been described following tamoxifen therapy, but the mechanisms for resistance to aromatase inhibitors (AI) remain less well known.

HYPOTHESIS Estrogen deprivation results in altered methylation and altered expression of critical target genes in breast cancer cells, which helps the cell to survive in the absence of estrogen, contributing to acquired AI resistance in breast cancer patients.

MATERIALS AND METHODS We utilized derivatives of the ER_ MCF-7 cell line which were isolated after being cultured in estrogen-free media for 9 months (C4-12 cell line) and 18–24 months (LTED, Long term estrogen deprivation cell line). A genome-wide methylation screen was performed using Methyl CpG binding Domain (MBD) pull down assay followed by hybridization into Affymetrix Human Promoter 1.0R Array. Altered DNA methylation was validated by bisulfite genomic sequencing assays while gene expression of candidate genes was studied by qRT-PCR and Western blotting.

RESULTS There were a significant amount of differentially methylated genes in C4-12 and LTED when compared to MCF7. Intriguingly, among the genes which were significantly hypomethylated in both endocrine resistant cell lines were a number of histone genes, with the homomorphic variant HIST1H2BE showing the strongest hypomethylation. Canonical histones have both homomorphic and heteromorphic variants, which differ in their timing of expression and similarity to the canonical histone protein's amino acid sequence. Overexpression of various heteromorphic histone variants have been implicated in carcinogenesis, but to date, there have been no studies on homomorphic variants, and specifically H2B variants, in regards to their role in tumorigenesis. We show that hypomethylation of HIST1H2BE was associated with its upregulation in C4-12 and LTED cells. Furthermore, knockdown of of HIST2BE resulted in decreased growth in the endocrine resistant cells, but not in the parental MCF-7 cell lines.

CONCLUSION & FUTURE DIRECTIONS The study is novel in two ways; first, this is the first study to show a potential role for histone variants in endocrine resistance. Second, this is one of very few examples where hypomethylation (instead of hypermethylation) results in altered expression of genes critical in tumorigenesis. Current studies include the detailed characterization of the phenotype following over-expression and knockdown of HIST1H2BE, the examination of the timing of expression of this variant in the S phase, and finally we are measuring methylation and expression of HIST2BE in a large collection of tumors from AI-treated breast cancer patients.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-09-02.

Parity-induced decrease in systemic growth hormone alters mammary gland signaling: a potential role in pregnancy protection from breast cancer

Early full-term pregnancy is an effective natural protection against breast cancer in both humans and experimental rodents. The protective effect of an early pregnancy is, in part, linked to changes in circulating hormones that are involved in both normal breast development and breast cancer. For example, a reduction in circulating growth hormone (GH) has been shown to protect rats from carcinogen-induced mammary tumors. We examined the ability of a full-term pregnancy to alter the endocrine GH/insulin-like growth factor-I (IGF-I) axis and how this change affected normal mammary gland function in two commonly used rat models (Sprague-Dawley and Wistar Furth). Circulating GH and IGF-I were measured in blood drawn every 30 minutes from parous and age-matched virgin female rats. Mean serum GH levels were significantly decreased (P < 0.01) in parous compared with age-matched virgin rats for both strains. Changes in GH levels were independent of estrous cycle, indicated by a significant (P < 0.05) reduction in circulating levels of GH during estrus and diestrus in both parous strains. Despite the decrease in circulating GH, pituitary GH mRNA levels were unaltered in parous rats. Circulating IGF-I and hepatic IGF-I mRNA were also unaltered by parity in either rat strain. Immunoblot analysis of mammary glands showed decreases in phosphorylation of signal transducer and activator of transcription 5A and Janus-activated kinase 2, suggesting reduced action of GH in the mammary gland. Therefore, although the parity reduction in circulating GH does not affect circulating IGF-I levels, it is possible that reduced GH acts directly at the mammary gland and may play a role in pregnancy protection from breast cancer.

Estrogen Deprivation Results in Altered DNA Methylation Profile in Breast Cancer Cells – Role in Endocrine Resistance?

Postmenopausal breast cancer patients benefit from aromatase inhibitors (AIs) that reduce the levels of estrogens which are critical for tumor growth. To date, epigenetic contributions to hormonal therapy resistance have not been well characterized, with only a limited understanding of antiestrogen mediated epigenetic modification of chromatin and altered gene expression. Furthermore, no genome-wide studies have been undertaken to identify altered DNA methylation patterns due to estrogen deprivation, which mimic AI therapy. We hypothesized that estrogen deprivation results in altered methylation, and therefore altered expression of critical target genes in breast cancer cells, which ultimately helps the cell to survive in the absence of estrogen and thus would contribute to acquire AI resistance in breast cancer patients.We used previously established MCF-7 cell clones, termed C4-12 and LTED (Long Term Estrogen Deprivation) that were isolated after being cultured in estrogen-free media for 9 months and 18-24 months, respectively. A genome-wide methylation screen was done using Methyl CpG binding Domain (MBD) pull down assay followed by hybridization into Affymetrix Human Promoter 1.0R Array. Altered DNA methylations were validated by bisulfite genomic sequencing assays and gene expression of some selected genes were studied by qRT PCR.From the array, we found that long term estrogen deprivation results in widespread genomic hyper- and hypomethylation events. 267 and 301 genes were hypermethylated in C4-12 and LTED respectively. In both resistant cell lines, the number of hypermethyled genes was more prominent than hypomethylated genes since only 82 and 97 genes were hypomethylated in C4-12 and LTED respectively. While hypomethylation of genes generally correlated with increased gene expression, hypermethylation did not in many cases. A gene which was heavily methylated in both cell line system, possibly reflecting a more general and important pathway in estrogen-deprivation, was HOXC10. Transient and stable silencing of HOXC10 in MCF-7 cells resulted in increased cell proliferation in estrogen deprived medium, suggesting a potential role of HOXC10 in developing resistance to endocrine therapy.This is the first genome-wide approach to identify gene-specific epigenetic alterations, and the functional consequences of these changes in developing resistance to estrogen deprivation therapy. This approach allows the development of epigenetic signatures of therapeutic resistance to be used concurrently with genomic signatures to better understand the molecular mechanism of endocrine resistance. This study might provide the basis for future clinical trials such as combination therapy of DNA demethylating agents and aromatase inhibitors.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5127.

Progesterone Receptor (PR) Promoter Methylation – Role as a Predictive and Prognostic Marker in Breast Cancer

Estrogen receptor α expression is a well known and clinically utilized predictor of endocrine treatment response. In addition, loss of expression of the progesterone receptor (PR), an estrogen induced gene, has been shown to be associated with resistance to endocrine therapy. PR is known to be epigenetically regulated by DNA methylation, but only a few studies have correlated PR DNA methylation with its expression in breast cancer. Previous studies are contradictory and have been limited by small sample size. There is also evidence that differential expression of the two PR isoforms, PRA and PRB, might contribute to breast tumorigenesis, and altered hormone response. Whether PRA and/or PRB DNA methylation could predict response to endocrine therapy remains an open question. Further, there are no published studies so far testing whether PRA and/or PRB methylation have prognostic significance.Our objective was 1) to determine whether there was an association between PRA and/or PRB methylation levels with total PR expression in breast tumors, and 2) to determine if PRA and/or PRB methylation would have predictive and/or prognostic value. For this study, we utilized tumor DNA from patients with ER-positive breast tumors which were treated with adjuvant tamoxifen after surgery (n=500), and from patients treated with surgery only (n=500). PR expression was determined by ligand binding assay, and PRA and PRB promoter methylation was measured by bisulfite pyrosequencing.Both PRA and PRB methylation were significantly (p&lt;0.0001) associated with PR expression, in an inverse relationship. Low PR expression was significantly (p=0.02) associated with worse overall survival (OS), and there was a trend towards shorter disease free survival (DFS) in the tamoxifen treated group. There was no association between PR expression and survival in the untreated group. PRA methylation was significantly (p&lt;0.0001) associated with PRB methylation. Intriguingly, increased PRA methylation was significantly associated with shorter DFS (p=0.047) and OS (p=0.0067) in tamoxifen treated patients, and with shorter OS (p=0.008) in the untreated patients. In contrast, there was no significant association between PRB methylation and survival in either tamoxifen treated or untreated patients.Our results show that PR expression is significantly associated with PR methylation. The data suggest that PRA methylation is a predictive marker for tamoxifen response and also a prognostic marker for breast cancer progression. This is the largest study so far to elucidate the association of PRA and PRB methylation with PR status, response to tamoxifen, and tumor prognosis, and we believe that it provides useful insights into the role of PR methylation in breast tumorigenesis.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2002.

Concussion: comparison of humans and rats

Concussion is the most primitive and probably the most simple central nervous system response to an outside agent. Although millions of neurons undergo a very rapid reversal with loss and restoration of function, many physicians argue that every knockout blow leaves some residual damage, i.e., some or all of these neurons stop short of recovery. Clinical experience shows a wide discrepancy in the appearance or persistence of certain signs and symptoms after all types of head injury, but particularly after concussing blows, when third party or grievance cases are involved. Using slow motion filmstrips of boxing ring knockouts, we established a grading system for concussion and duplicated these grades in nonanesthetized rats. When we compared the performance, learning, and memory of concussed rats with their preconcussion performance and with the performance of nonconcussed controls, we were unable to find any differences.